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Dear developers.
I have a Windows 11 ASUS TUF machine with 2 GPUs . There is NVIDIA GTX1650 and CUDA 12.0 installed on it. I have installed WSL2 to work in the linux environment. I compiled the Auto…
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XCA should be doing the downloading of files from the PDB. Including extracting event maps, if they were uploaded.
This won't be hard, just needs working out a few arcane details of where to fin…
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One of the recurring errors I've seen (using Perses 0.8.1, in my slightly janky Docker container)
Result: the atom mapping fails, and the edge does not run
```
Traceback (most recent call last)…
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Should look something like this in the end:
```typescript
export type LigandBindingSite = {
source_object:{
rcsb_id: ..., //
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Hey @samsledje !
Thanks for the great work you are doing, it's really a powerful idea to apply protein-ligand similarity search for virtual screening.
According to the results of your current stat…
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Currently all our docking workflows assume/require that you are docking to an ASAP target, and do some stuff with the structures you passed under these assumptions. I think it would be nice to have so…
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In the Nichenet model, if a target gene is repressed by a ligand-receptor interactions is it considered a target? Or does the model only take into account cases where ligand-receptor has a positive/ac…
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Transformations from ligand 0 to ligands 56-60 appear to have failed:
JSON entries
```JSON
"55": {
"JOBID": 55,
"directory": "RUN54",
"end": 56,
"ff": "…
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Representations are not restored because there is a crash during the restore process when it tries to assign a representation to an ngl object that was deleted in previous step.
Steps to reproduce:…
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Several laboratories would like to use YANK for computing free energy differences upon protein mutations, either for peptide ligands or protein targets.
This functionality would require a way to modi…